Building on Neil Whitehead’s work in northern South America, this article considers the formations of two different deep-forest regional networks. Though these Amerindian spaces have origins in the precolonial past, this article analyses their shaping in the seventeenth and eighteenth centuries, a period when they were invaded by colonial agents. There were other regional systems along the course of the Amazon and its many tributaries that were a part of a similar historical process of refounding identities and claims on land and people involving challenges to leadership and political organization. Following Hal Langfur, we can term this general making of spaces a re-territorialization. Critical social relations include those between Amerindian ethnic entities and their leaders, soldiers, and missionaries. This article focuses on a key spatial relation between Amerindian settlements and the mission, or partially colonized village, which had an indirect or direct contact with each other.